We have explored transcriptional patterns associated with spontaneous cancer development and chemically-induced carcinogenesis. In these studies, it is necessary to control mixed directional false discovery rate due to the fact that we tested for multiple comparisons and there is a potential for directional errors when declaring genes to be up- or downregulated. Gene expression patterns from spontaneous tumors arising in untreated F344/N rats were compared with samples from untreated age-matched control animals. Upregulated genes were associated with growth factors, oncogenes, cytokines, and pathogen-associated molecular patterns receptors. In addition, the production of reactive oxygen and nitrogen species was affected (Blackshear et al., 2013). Apoptosis pathways were downregulated. Global gene expression patterns of tumors arising in response to the toxicant Vinylidene Chloride were compared to spontaneous mesotheliomas and F344/N rat mesothelial cells (Fred-PE) in order to discover the functions associated with VDC exposure. The data produced from VDC-treated animals suggested that exposure to this asbestos-related chemical is associated with the gene regulation of oncogenes, growth factors, and cell cycle response (Blackshear et al., 2014). In a different study, we evaluated the molecular profiles associated with sleep and sleep deprivation in heart and lung tissues. DNA microarrays were used to compare gene expression in tissue from sleeping and sleep deprived mice. A total of 3% and 6% of the measured transcripts were shown to be sleep specific in the lung and heart, respectively. Processes associated with cellular stress and protein folding were reduced with sleep, while tissue-specific metabolic processes were enhanced with sleep (Anafi et al., 2013).